Hello,
I wonder if there was any direct answer to the question that Lari made a
couple of days ago.
Sorry if I missed it, but I believe there wasn't any response to the
ccp4bb...
thanks
Alejandro
Lari Lehtio wrote:
> Dear All,
>
> I just came back from the beam line and started to continue my work on a structure that I solved
> while collecting other data. I noticed that my R-factors were a lot higher at home lab although
> I was using the exact same input files.
>
> I then noticed that the version was different:
>
> The one giving lower R-factors was
> Refmac_5.2.0019 version 5.2.0019 : 06/09/05
>
> And the one giving higher:
> Refmac_5.3.0032 version 5.3.0032 : 02/16/06
>
> I happened to have the older version also in my home pc, so I tried again and indeed, 5.2.0019
> gives lower R-factors.
>
> The input command is identical, but when I "diffed" the pdb-files, I noticed that anisotropic
> scale is missing in the newer files. Did I make a mistake? How can I turn it back on.
>
> Below is the diff output and the command used for refmac.
>
> Thank you in advance,
>
> ~L~
>
> < REMARK 3 PROGRAM : REFMAC 5.2.0019
>
>> REMARK 3 PROGRAM : REFMAC 5.3.0032
>>
> < REMARK 3 R VALUE (WORKING + TEST SET) : 0.21101
> < REMARK 3 R VALUE (WORKING SET) : 0.20867
> < REMARK 3 FREE R VALUE : 0.25559
>
>> REMARK 3 R VALUE (WORKING + TEST SET) : 0.23077
>> REMARK 3 R VALUE (WORKING SET) : 0.22807
>> REMARK 3 FREE R VALUE : 0.28228
>>
> < REMARK 3 BIN R VALUE (WORKING SET) : 0.240
>
>> REMARK 3 BIN R VALUE (WORKING SET) : 0.262
>>
> < REMARK 3 BIN FREE R VALUE : 0.288
>
>> REMARK 3 BIN FREE R VALUE : 0.343
>>
> < REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.271
>
>> REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.941
>>
> < REMARK 3 B11 (A**2) : 2.35
> < REMARK 3 B22 (A**2) : -1.99
> < REMARK 3 B33 (A**2) : 0.32
>
>> REMARK 3 B11 (A**2) : 0.00
>> REMARK 3 B22 (A**2) : 0.00
>> REMARK 3 B33 (A**2) : 0.00
>>
> < REMARK 3 B13 (A**2) : 0.90
>
>> REMARK 3 B13 (A**2) : 0.00
>>
>
> _____________________________________________________________________________________
> make check NONE
> make -
> hydrogen YES -
> hout NO -
> peptide NO -
> cispeptide YES -
> ssbridge YES -
> symmetry YES -
> sugar YES -
> connectivity NO -
> link NO
> refi -
> type REST -
> resi MLKF -
> meth CGMAT -
> bref ISOT
> ncyc 10
> scal -
> type SIMP -
> reso 2.100 19.976 -
> LSSC -
> ANISO -
> EXPE
> solvent YES -
> VDWProb 1.4 -
> IONProb 0.8 -
> RSHRink 0.8
> weight -
> MATRIX 0.1
> monitor MEDIUM -
> torsion 10.0 -
> distance 10.0 -
> angle 10.0 -
> plane 10.0 -
> chiral 10.0 -
> bfactor 10.0 -
> bsphere 10.0 -
> rbond 10.0 -
> ncsr 10.0
> labin FP=FP SIGFP=SIGFP -
> FREE=FreeRflag
> labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
> PNAME unknown
> DNAME unknown130907
> RSIZE 80
> END
>
> _______________________________________
>
> Lari Lehtiö
> Structural Genomics Consortium
> Medical Biochemistry & Biophysics Dept.
> Karolinska Institute
> Stockholm, Sweden
> _______________________________________
>
>
>
--
Alejandro Buschiazzo, PhD
Research Scientist
Laboratory of Structural Biology
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +5982 5220910 int. 120
Fax: +5982 5224185
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